I have 2 questions (1 regarding DADA2 and 1 regarding taxonomy results). They are short questions so I put them in the same post. Thanks for your help!
I ran the DADA2 denoise pipeline followed by the core-metrics-phylogeny command to obtain alpha and beta diversity indices. I noticed that the observed-otu command gives number of OTUs (in this case ASVs because I am using DADA2) between 80 to 120 for my samples. My samples are soil samples, I was wondering if it was too low a number?
I ran my taxonomic analysis using the 99_otus fasta and taxonomy file from the gg_13_8 database. I retrained my classifier with my primer set (also because the scikit package was incompatible). I noticed there are some taxonomic annotations with no information from the phyla level down to the species level. (E.g. k_Bacteria;p__;c__;o__;f__;g__;s__)
The number of these annotations are really low, yet I was wondering why so. Are these the unknown samples?